Nucleocapsid protein preferentially binds the stem-loop of duplex/quadruplex hybrid that unfolds the quadruplex structure.

NCp7 protein binds the duplex/quadruplex hybrid structure, which decreases the thermal stability of DNA and unfolds the G-quadruplex structure. Interestingly, the duplex in the stem-loop region is the more favorable binding site of NCp7. The NCp7 binding twists the top G-tetrad, weakens hydrogen bonding and causes K+ ejection, hence disrupting the G4 structure.